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- PDB-5tih: Structural basis for inhibition of erythrocyte invasion by antibo... -

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Basic information

Entry
Database: PDB / ID: 5tih
TitleStructural basis for inhibition of erythrocyte invasion by antibodies to Plasmodium falciparum protein CyRPA
Components
  • CyRPA antibody Fab Heavy Chain
  • CyRPA antibody Fab Light Chain
  • Cysteine-rich protective antigen
KeywordsIMMUNE SYSTEM / Plasmodium falciparum CyRPA Inhibitory antibody
Function / homology
Function and homology information


microneme lumen / microneme / symbiont entry into host / apical part of cell / cytoplasmic vesicle / host extracellular space / host cell plasma membrane / protein-containing complex / extracellular region / plasma membrane
Similarity search - Function
Cysteine-rich protective antigen 6 bladed domain / Cysteine-Rich Protective Antigen 6 bladed domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Cysteine-rich protective antigen
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.44 Å
AuthorsChen, L. / Xu, Y. / Wang, W. / Thompson, J.K. / Goddard-Borger, E. / Lawrence, M.C. / Cowman, A.F.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Elife / Year: 2017
Title: Structural basis for inhibition of erythrocyte invasion by antibodies toPlasmodium falciparumprotein CyRPA.
Authors: Chen, L. / Xu, Y. / Wong, W. / Thompson, J.K. / Healer, J. / Goddard-Borger, E.D. / Lawrence, M.C. / Cowman, A.F.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Feb 21, 2018Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine-rich protective antigen
H: CyRPA antibody Fab Heavy Chain
L: CyRPA antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5396
Polymers86,3613
Non-polymers1773
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.950, 87.380, 145.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine-rich protective antigen


Mass: 39485.402 Da / Num. of mol.: 1 / Fragment: UNP residues 30-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF3D7_0423800 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IFM8
#2: Antibody CyRPA antibody Fab Heavy Chain


Mass: 23343.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody CyRPA antibody Fab Light Chain


Mass: 23532.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5 / Details: 11% PEG5000 monomethyl ether 0.2M NaAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.44→38.339 Å / Num. obs: 38349 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.964 % / Biso Wilson estimate: 54.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.089 / Χ2: 0.983 / Net I/σ(I): 14.54 / Num. measured all: 228722 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.44-2.585.6190.9912.1732264586957420.7271.08897.8
2.58-2.766.2050.6293.5536547589358900.8660.68799.9
2.76-2.986.1960.3276.1733512541154090.9570.357100
2.98-3.266.1690.15911.0930618496849630.990.17399.9
3.26-3.656.0980.08518.4228270463946360.9960.09399.9
3.65-4.215.9950.05725.6523991401740020.9970.06299.6
4.21-5.145.810.04331.7219864343834190.9980.04899.4
5.14-7.235.5890.04431.3515186272627170.9980.04899.7
7.23-38.3395.3910.03534.58470162915710.9990.03896.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5l9d
Resolution: 2.44→38.339 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 1891 4.93 %
Rwork0.1887 36454 -
obs0.1898 38345 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.44 Å2 / Biso mean: 68.0314 Å2 / Biso min: 30.38 Å2
Refinement stepCycle: final / Resolution: 2.44→38.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5990 0 12 43 6045
Biso mean--68.68 51.99 -
Num. residues----750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036149
X-RAY DIFFRACTIONf_angle_d0.5768343
X-RAY DIFFRACTIONf_chiral_restr0.045914
X-RAY DIFFRACTIONf_plane_restr0.0031064
X-RAY DIFFRACTIONf_dihedral_angle_d13.0493675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4401-2.50110.2961200.28372495261596
2.5011-2.56870.32341310.294125742705100
2.5687-2.64430.38991340.285325812715100
2.6443-2.72960.27171450.255125452690100
2.7296-2.82720.25691290.254626042733100
2.8272-2.94030.27071310.24425812712100
2.9403-3.07410.2461390.234625942733100
3.0741-3.23610.30031220.236526222744100
3.2361-3.43870.2351260.2125972723100
3.4387-3.7040.2531500.200226052755100
3.704-4.07640.18661390.178426202759100
4.0764-4.66540.15581270.14272633276099
4.6654-5.87440.16111370.14626682805100
5.8744-38.34360.17261610.15352735289698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.0894-0.37920.05624.01322.67565.2269-0.22020.0644-0.01160.2018-0.03390.23810.2526-0.170.21810.4077-0.0616-0.03180.27560.06620.361972.282470.897193.0159
22.90620.10790.72513.9345-1.70855.5853-0.08220.2948-0.1685-0.28950.1897-0.43140.19940.4643-0.09530.3812-0.08880.02210.3203-0.05820.400789.322567.000893.4131
34.4771-2.2155-0.08232.21141.43292.5658-0.1628-0.55730.05180.43510.11780.23410.1518-0.0920.02480.49420.00170.03780.339-0.01160.416679.806471.6032111.4923
42.92651.27191.36295.33692.03276.93540.263-0.1607-0.64660.5834-0.0467-0.30770.69530.1931-0.24330.46930.0226-0.08250.30790.00290.52770.539347.798270.6755
50.356-0.3751-0.56151.46661.03197.5764-0.05460.3129-0.1398-0.02380.1096-0.02440.81470.7449-0.05050.44080.1071-0.070.5889-0.12340.590773.421947.427548.9513
65.09711.3139-4.11935.443-2.17576.80320.1174-0.4066-0.0895-0.1432-0.083-0.58530.63121.95130.02970.53780.1509-0.02171.1704-0.23360.500680.923145.283335.0116
75.8209-0.1465-1.97263.8240.4097.2081-0.04070.63340.1904-0.56040.11930.0613-1.2055-0.055-0.0860.5681-0.1195-0.07260.378-0.00340.374467.449971.044561.078
84.27982.7820.57936.2274-0.6735.6162-0.09340.35530.235-0.33040.1914-0.3789-0.6940.8476-0.11140.4392-0.11330.00760.4518-0.02860.35373.750368.904463.7737
92.07282.15791.20018.46484.68598.22150.16520.14190.0373-0.2385-0.05130.041-0.39220.7599-0.17420.4678-0.00240.07610.7302-0.1090.430471.103457.203231.8898
102.68621.95211.11952.9133.61957.6803-0.01680.3567-0.1191-1.3982-0.06790.4767-0.57320.01830.05990.70130.071-0.05330.8387-0.11340.542466.56953.23322.1192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 109 )A2 - 109
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 180 )A110 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 333 )A181 - 333
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 83 )H1 - 83
5X-RAY DIFFRACTION5chain 'H' and (resid 84 through 144 )H84 - 144
6X-RAY DIFFRACTION6chain 'H' and (resid 145 through 215 )H145 - 215
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 38 )L1 - 38
8X-RAY DIFFRACTION8chain 'L' and (resid 39 through 102 )L39 - 102
9X-RAY DIFFRACTION9chain 'L' and (resid 103 through 174 )L103 - 174
10X-RAY DIFFRACTION10chain 'L' and (resid 175 through 212 )L175 - 212

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